Distribution of Beta Lot Data By Instrument/Operator
Dilsher Singh Dhillon
15 February,2022
Introduction
Using data uptill 25th January
pate-rnd xmap-collector --include_file_str 20220119_WC_P1vP6 \
--include_file_str 20220120_ShakeSpd_1000rpm_Panel1_Plate1 \
--include_file_str 20220120_ShakeSpd_1200rpm_Panel1_Plate2 \
--include_file_str 20220120_ShakeSpd_1500rpm_Panel1_Plate3 \
--include_file_str 20220120_ShakeSpd_1000rpm_Panel2_Plate1 \
--include_file_str 20220120_ShakeSpd_1200rpm_Panel2_Plate2 \
--include_file_str 20220120_ShakeSpd_1500rpm_Panel2_Plate3 \
--include_file_str 20220120_ShakeSpd_1200rpm_Panel2_Plate2 \
--include_file_str 20220120_ShakeSpd_1500rpm_Panel2_Plate2 \
--include_file_str Beta \
--include_file_str Interf \
--include_file_str PltStd \
--include_file_str Endogenous \
--include_file_str Exogenous \
--include_file_str Platinum \
--include_file_str Reproducibility \
--include_file_str Donor_Screening \
--include_file_str PlatinumStd \
--include_file_str HamiltonEquiv\
--include_file_str ShakingCompare \
--include_file_str 20211221_DLS_Matrix_Int \
--include_sample_str Standard --include_sample_str Buffer --include_sample_str Background --include_sample_str QC --include_sample_str RC --ignore_case_sample \
--out_file_name betalot_experiments-2022-01-25.csvgsutil cp gs://inhouse-xmap-data/user_data_frames/betalot_experiments-2022-01-25.csv ~/'google drive'/'my drive'/projects/beta-av-testing/data/raw/beta-lot-stds-controls-2022-01-25.csvThis notebook aims to explore the distribution of Flexmaps and Hamiltons using the beta lot data. We will -
- Extract xMAP controls and standards data
- Extract the xmap log
- Match the batches we have available hamilton and flexmap information.
Note It looks like the log was only started to collect after 2021-12-02
raw .rmd file stored here
/home/ddhillon/dyson-sync/projects/beta-av-testing/notebooks/process-pseudo-guardbanding/notebooks/02.rmdData Import
xMAP Data
Using data uptill 25th January
Batches in xMAP
Log of instruments
Batches in log
Match the log of batches with the batches from xMAP data
Which ones match?
Which ones don’t match?
Some don’t match since the names aren’t exactly the same - we will change these manually. There are still some we’re not able to retrieve xmap data on.
xmap_batches %>%
mutate(batch = case_when(batch == "20211214_ShakeComp_Auto_Beta_Panel2_B3" ~ "20211214_ShakingCompare_Auto_Beta_Panel2",
batch == "20211214_Shake_Workcell_Beta_Panel2_B1.csv" ~ "20211214_ShakingCompare_Workcell_Beta_Panel2",
batch == "20211214_Shake_Workcell_Beta_Panel2_B2" ~ "20211214_ShakingCompare_Workcell_Beta_Panel2",
batch == "20211214_Shake_Workcell_Beta_Panel2_B3" ~ "20211214_ShakingCompare_Workcell_Beta_Panel2",
batch == "20211214_Shaking_Auto_Beta_Panel1_B1" ~ "20211214_ShakingCompare_Auto_Beta_Panel1",
batch == "20211214_Shaking_Auto_Beta_Panel1_B2" ~ "20211214_ShakingCompare_Auto_Beta_Panel1",
batch == "20211214_Shaking_Auto_Beta_Panel1_B3" ~ "20211214_ShakingCompare_Auto_Beta_Panel1",
batch == "20211214_Shaking_Workcell_Beta_Panel1_B1" ~ "20211214_ShakingCompare_Workcell_Beta_Panel1",
batch == "20211214_Shaking_Workcell_Beta_Panel1_B2" ~ "20211214_ShakingCompare_Workcell_Beta_Panel1",
batch == "20211214_Shaking_Workcell_Beta_Panel1_B3" ~ "20211214_ShakingCompare_Workcell_Beta_Panel1",
batch == "20210111_PltStd2_Panel1_P3_B1" ~ "20220111_PltStd2_Panel1_P3",
batch == "20210111_PltStd2_Panel1_P3_B2" ~ "20220111_PltStd2_Panel1_P3",
batch == "20210111_PltStd2_Panel1_P3_B3" ~ "20220111_PltStd2_Panel1_P3",
batch == "20220111_PltStd2_Panel2_P3_B1" ~ "20220111_PltStd2_Panel2_P3",
batch == "20220111_PltStd2_Panel2_P3_B2" ~ "20220111_PltStd2_Panel2_P3",
batch == "20220111_PltStd2_Panel2_P3_B3" ~ "20220111_PltStd2_Panel2_P3",
batch == "20220119_WC_P1vP6_P2_Plate2" ~ "20220119_WC_P1vP6_P2_plate2",
TRUE ~ as.character(batch))) %>%
inner_join(log_batches)NOTE
Batches not in pate
1. 20211221_DLS_Matrix_Int_
2. 20220113_1500Shake_TS_
3. 20220124_BufferAdditives_
4. 20220201_AdditivesStds_
Update the above plots after adding this in
Strings that are still not matching
Operator information?
Can we also add in operator information to these experiments?
## # A tibble: 66 × 7
## date operator batch description panel_name panel_lot_number
## <date> <chr> <chr> <chr> <list> <list>
## 1 2021-12-02 Connor 2021… 20211202_M… <chr [1]> <dbl [1]>
## 2 2021-12-02 Tyler M 2021… 20211202_M… <chr [1]> <dbl [1]>
## 3 2021-12-06 Connor 2021… 20211206_E… <chr [1]> <dbl [1]>
## 4 2021-12-06 Connor 2021… 20211206_E… <chr [1]> <dbl [1]>
## 5 2021-12-06 Tyler M 2021… 20211206_E… <chr [1]> <dbl [1]>
## 6 2021-12-06 Tyler M 2021… 20211206_E… <chr [1]> <dbl [1]>
## 7 2021-12-14 Connor 2021… 20211214_S… <chr [1]> <dbl [1]>
## 8 2021-12-14 Connor 2021… 20211214_S… <chr [1]> <dbl [1]>
## 9 2021-12-14 Tyler M 2021… 20211214_S… <chr [1]> <dbl [1]>
## 10 2021-12-14 Tyler M 2021… 20211214_S… <chr [1]> <dbl [1]>
## # … with 56 more rows, and 1 more variable: instrument_name <chr>Viz
QCs
Which experiments had QCs on them?
10 experiments?
5 experiments had RCs on them (log was started on 20211202 so any experiments with RCs on them prior to that aren’t in this list currently)
We have more data on the latest controls so we will look at those
Plots out all the RCs for each flexmap and hamilton
Flexmap x-axis
FLT3L
IL-1 R2
IL-8
MUC-16
CEA
TNC
WFDC2
[[1]] NULL
[[2]] NULL
[[3]] NULL
[[4]] NULL
[[5]] NULL
[[6]] NULL
[[7]] NULL
Hamilton x-axis
FLT3L
IL-1 R2
IL-8
MUC-16
CEA
TNC
WFDC2
[[1]] NULL
[[2]] NULL
[[3]] NULL
[[4]] NULL
[[5]] NULL
[[6]] NULL
[[7]] NULL
Recoveries
Experiments with recoveries
Flexmap x-axis
FLT3L
IL-1 R2
IL-8
MUC-16
CEA
TNC
WFDC2
[[1]] NULL
[[2]] NULL
[[3]] NULL
[[4]] NULL
[[5]] NULL
[[6]] NULL
[[7]] NULL
Hamilton x-axis
FLT3L
IL-1 R2
IL-8
MUC-16
CEA
TNC
WFDC2
[[1]] NULL
[[2]] NULL
[[3]] NULL
[[4]] NULL
[[5]] NULL
[[6]] NULL
[[7]] NULL
Operator specific comparison
FLT3L
IL-1 R2
IL-8
MUC-16
CEA
TNC
WFDC2
[[1]] NULL
[[2]] NULL
[[3]] NULL
[[4]] NULL
[[5]] NULL
[[6]] NULL
[[7]] NULL
Bead counts
Flexmap x-axis
Hamilton x-axis
FLT3L
IL-1 R2
IL-8
MUC-16
CEA
TNC
WFDC2
[[1]] NULL
[[2]] NULL
[[3]] NULL
[[4]] NULL
[[5]] NULL
[[6]] NULL
[[7]] NULL